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@@ -1,7 +1,4 @@
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-#
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-
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-Interneurons in the subiculum have a polarized axonal cloud instead of a circular as found in other brain regions. Additionally, pyramidal neurons in the subiculum lack recurrent connections, but they connect via recurrent inhibition. Therefore, inhibition plays a major role in this circuitry and we pose the question, which function the extraordinary axon morphology serves in this setting.
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-
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+# Spatially structured perisomatic inhibition organized along polarized fast-spiking interneuron axons
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### How to setup the python environment
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@@ -22,40 +19,30 @@ To run the scripts, you also need to make the repository folder available in the
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conda develop .
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```
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-If you need additional packages, install them via `conda install` and update the environment file via
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-
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-```bash
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-conda env export > environment.yml
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-```
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-
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-To update the existing environment
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-```bash
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-conda-env update -f environment.yml
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-```
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-
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### How to run the simulation
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-The entire process is split in three main scripts. The simulation is setup and run in
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+The entire process is split in three main scripts. The simulation is setup and run via
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```bash
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-run_simulation_perlin_map.py
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+python scripts/spatial_network/perlin_map/run_simulation_perlin_map.py
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```
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Relevant parameters are the range of scale and seed values for the input map generation as explained in the script.
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A preliminary analysis of the simulated data is done by running
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```bash
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-preliminary_analysis_perlin_map.py
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+python scripts/spatial_network/perlin_map/preliminary_analysis_perlin_map.py
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```
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The final analysis and figure generation is done by
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```bash
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-final_analysis_and_plotting_perlin_map.py
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+python scripts/spatial_network/perlin_map/final_analysis_and_plotting_perlin_map.py
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```
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Note, that running the simulation script will overwrite the saved data.
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The bulk of the runtime lies within the simulation and preliminary analysis which can be executed together via
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```bash
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-run_and_analyze_perlin.py
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+python scripts/spatial_network/perlin_map/run_and_analyze_perlin.py
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```
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after which the figure script can be tweaked and executed without loss of data.
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-For the supplement figure, a pinwheel map is used as an alternative input map. The run, analyse and plot scripts are organized in the same manner but found in the folder pinwheel_map.
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+For the supplement figure, a pinwheel map is used as an alternative input map. The run, analyse and plot scripts are
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+ organized in the same manner but found in the folder `scripts/spatial_network/supplement_pinwheel_map`.
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### Additional Ressources
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